buildCovMat: A function to build the covariate matrix of the constraints

In RCM: Fit row-column association models with the negative binomial distribution for the microbiome

Description

A function to build the covariate matrix of the constraints

Usage

buildCovMat(covariates, dat)

Arguments

covariates	the covariates, either as dataframe or as character string
dat	the phyloseq object In this case we will 1) Include dummy's for every level of the categorical variable, and force them to sum to zero. This is needed for plotting and required for reference level indepenent normalization. 2) Exclude an intercept. The density function f() will provide this already.

Value

a list with components

covModelMat	The model matrix
datFrame	The dataframe used to construct the model matrix

RCM documentation built on Nov. 8, 2020, 5:22 p.m.